All sorts of issues! please help!

[Mountaindewbot]

So Ive got a 93 325is and its history is I bought it and two weeks later I totaled it, I got it back and running within weeks. but the motor always ran like it was missing a cylinder eventally it came down to the motor and tranny had +300,000 miles they were both leaking fluids and it was just slowly dying.

so I replaced it with a newer younger engine and tranny but now its doing the shudder,stalling thing again and its not even all of the time 1 minute its running like a champ the next its chugging. You can literaly feel the change. Its not the motor doing this it has to be an outside source. any Idea's?

the second is the driver door window, it works intermitantly and expecially when its fully down. I can hear a clicking noise when I push the up button. I think somthing is jamming it but I cant find anything.

I'm frusterated and I'm having issues naming off all of the problems so I'll just leave it at this and maybe add more when issues arise.

[94325is]

I have a problem with the passenger window that sounds similar... I am told that it is a sensor in the door that needs replacing, so it is fp and disconnected so it will not get stuck down again... had too many cold winter rides, and rain scares... your engine woes sound very similar to mine... if I find anything, I'll let you know...

[PrInG]

I have a similar issue with my passenger side window as well except mine gets stuck up =/ I'm probably going to pull the sensor out of the door and clean it this weekend. NO AC in the summer is not good =/
As for motor issues. I'd check for vacuum leaks first. Something Ive learned is that vacuum leaks can cause a lot of issues. Check the little guy that connects your ICV to your intake manifold. It was always an issue for me. good luck